X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FConsensusThread.java;h=284f1a164b28c03ca351b6214fe2cd9704cc43d3;hb=ccfe63de177540228855a8361ed0f46061830aea;hp=5c55d48455e1b4cdf8fdb3b4c484838363711a2a;hpb=6dd2a0e7f175aea6f16ded581d7e97f263f7875d;p=jalview.git

diff --git a/src/jalview/workers/ConsensusThread.java b/src/jalview/workers/ConsensusThread.java
index 5c55d48..284f1a1 100644
--- a/src/jalview/workers/ConsensusThread.java
+++ b/src/jalview/workers/ConsensusThread.java
@@ -28,7 +28,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ProfilesI;
 import jalview.datamodel.SequenceI;
-import jalview.schemes.ColourSchemeI;
+import jalview.renderer.ResidueShaderI;
 
 public class ConsensusThread extends AlignCalcWorker
 {
@@ -119,7 +119,8 @@ public class ConsensusThread extends AlignCalcWorker
     AlignmentAnnotation consensus = getConsensusAnnotation();
     consensus.annotations = new Annotation[aWidth];
     AlignmentAnnotation gap = getGapAnnotation();
-    if (gap!=null) {
+    if (gap != null)
+    {
       gap.annotations = new Annotation[aWidth];
     }
   }
@@ -132,8 +133,8 @@ public class ConsensusThread extends AlignCalcWorker
 
     SequenceI[] aseqs = getSequences();
     int width = alignment.getWidth();
-    ProfilesI hconsensus = AAFrequency.calculate(aseqs, width, 0,
-            width, true);
+    ProfilesI hconsensus = AAFrequency.calculate(aseqs, width, 0, width,
+            true);
 
     alignViewport.setSequenceConsensusHash(hconsensus);
     setColourSchemeConsensus(hconsensus);
@@ -152,11 +153,10 @@ public class ConsensusThread extends AlignCalcWorker
    */
   protected void setColourSchemeConsensus(ProfilesI hconsensus)
   {
-    ColourSchemeI globalColourScheme = alignViewport
-            .getGlobalColourScheme();
-    if (globalColourScheme != null)
+    ResidueShaderI cs = alignViewport.getResidueShading();
+    if (cs != null)
     {
-      globalColourScheme.setConsensus(hconsensus);
+      cs.setConsensus(hconsensus);
     }
   }
 
@@ -221,29 +221,26 @@ public class ConsensusThread extends AlignCalcWorker
 
     long nseq = getSequences().length;
     AAFrequency.completeConsensus(consensusAnnotation, hconsensus,
-            hconsensus.getStartColumn(),
-            hconsensus.getEndColumn() + 1,
+            hconsensus.getStartColumn(), hconsensus.getEndColumn() + 1,
             alignViewport.isIgnoreGapsConsensus(),
             alignViewport.isShowSequenceLogo(), nseq);
   }
-    /**
-     * Convert the computed consensus data into a gap annotation row for
-     * display.
-     * 
-     * @param gapAnnotation
-     *          the annotation to be populated
-     * @param hconsensus
-     *          the computed consensus data
-     */
-    protected void deriveGap(AlignmentAnnotation gapAnnotation,
-            ProfilesI hconsensus)
-    {
 
-      long nseq = getSequences().length;
-      AAFrequency.completeGapAnnot(gapAnnotation, hconsensus,
+  /**
+   * Convert the computed consensus data into a gap annotation row for display.
+   * 
+   * @param gapAnnotation
+   *          the annotation to be populated
+   * @param hconsensus
+   *          the computed consensus data
+   */
+  protected void deriveGap(AlignmentAnnotation gapAnnotation,
+          ProfilesI hconsensus)
+  {
+    long nseq = getSequences().length;
+    AAFrequency.completeGapAnnot(gapAnnotation, hconsensus,
             hconsensus.getStartColumn(), hconsensus.getEndColumn() + 1,
             nseq);
-
   }
 
   /**